EDIT: The issue described in the question is reproducible with version 1.31
of chemfig (from where the 'original definition' of the <->
arrow is taken). With version 1.34
ther issue does not occur any more and the desired output is obtained.
The following example contains a modified version of the <->
arrow type that does not show the gap if it is rotated by 180°
\documentclass{scrartcl}
\usepackage{chemfig}
\makeatletter
\definearrow3{<->}{%
\CF@arrow@shift@nodes{#3}%
\path(\CF@arrow@start@node)--(\CF@arrow@end@node)%
node[pos=0.5,sloped](\CF@arrow@start@node1){}node[pos=0.5,sloped](\CF@arrow@end@node1){};%
\expandafter\draw\expandafter[\CF@arrow@current@style](\CF@arrow@start@node1)--(\CF@arrow@end@node);%
\expandafter\draw\expandafter[\CF@arrow@current@style](\CF@arrow@end@node1)--(\CF@arrow@start@node);%
\CF@arrow@display@label{#1}{0.5}+\CF@arrow@start@node{#2}{0.5}-\CF@arrow@end@node
}
\makeatother
\begin{document}
\schemestart
\chemfig{*6(------)}
\arrow{<->}[0]
\chemfig{*6(------)}
\arrow{<->}[-90]
\chemfig{*6(------)}
\arrow{<->}[180]
\chemfig{*6(------)}
\schemestop
\end{document}

If you compare this with the original definition from chemfig.tex
\definearrow3{<->}{%
\CF@arrow@shift@nodes{#3}%
\path(\CF@arrow@start@node)--(\CF@arrow@end@node)%
node[pos=0.5,sloped,xshift=-1pt](\CF@arrow@start@node1){}node[pos=0.5,sloped,xshift=1pt](\CF@arrow@end@node1){};%
\expandafter\draw\expandafter[\CF@arrow@current@style](\CF@arrow@start@node1)--(\CF@arrow@end@node);%
\expandafter\draw\expandafter[\CF@arrow@current@style](\CF@arrow@end@node1)--(\CF@arrow@start@node);%
\CF@arrow@display@label{#1}{0.5}+\CF@arrow@start@node{#2}{0.5}-\CF@arrow@end@node
}
you can see, that I have removed the xshift
options.